GARANT COMMANDS: match - calculates match between two peak lists

usage: match <float> <float>

The list of measured peaks (read with the 'load peaks' command) and the
refence peaks (read with the 'load reference peaks' command) are matched
to each other. The match is written to the log, the assignment
of the measured peaks is copied to the matched reference peaks, and the
peak number of the measured peaks is copied to the comment field of the
matched reference peaks. The assigned reference peaks are used to 
calculated the chemical shifts of the coherences, which can be written
with the 'write coherences' command. 

The algortihm determines a one-to-one match that maximizes the target
function

        f = Sum (dij**p - t),						(1)

where the sum is over all pairs i,j of matched peaks, p are the first and
second of the two specified floating point parameters, respectively, and 
dij is the distance between the two peaks defined according to

        dij = - sqrt( {(w1i-w1j)/c1}**2 + {(w2i-w2j)/c2}**2 + ...)	(2)

In Eq. 2 w1i, w2i, w1j, w2j denote the position of peaks i and j in
all the dimensions of the spectrum, and c1 and c2 are scaling factors which
correspond to the variables <spectype>_matchf_w1, <spectype>_matchf_w2, ...

Note that the paramter, t, corresponds to a threshold value to exclude pairs of 
peaks with a large distance dij from the match.


EXAMPLE:

HNCO
   set HNCO_matchf_w1 = 10.0
   set HNCO_matchf_w2 =  1.0
   set HNCO_matchf_w3 =  2.0
   set HNCO_w1     = 1
   set HNCO_w2     = 2
   set HNCO_w3     = 3
  load peaks HNCO $dir/hnco.peaks
  load reference peaks HNCO $dir/hnco_pH9.peaks

set

load sequence $dir/gyrase.seq
make coherences			# generate all possible coherences
make couplings			# generate couplings
make peaks			# generate expected peaks

load assignments HNCO $dir/hnco.peaks $dir/gyrase.prot 0.0

match HNCO 2.0 -10.0

write coherences matched.prot

write reference peaks HNCO $dir/hnco_pH9_matched.peaks $dir/gyrase.prot

match HNCO 1.0 -10.0


see also: write refernce peaks, load peaks, match
